[R-sig-eco] adonis model specification

[Christine Griffiths]

Dear R helpers,

I have collected species composition data (counts of 24 species)from 16
plots. I am interested in seeing how different the plots are from each
other and how this changes over time.

My design is as follows: I repeatedly sampled the plots each month for 11
months. The plots are grouped into three treatments (1-3), which were
replicated 6 times (blocks 1-6). I have unbalanced data in that I lost 2
replicates from 2 of the treatments, so I have only 16 plots in total.

>From what I have read, I want to use the adonis function in the vegan
package. Having had a look at the set up of the dune data example, I have
set up my data in the same format. Below is an idea of my data.
I have 16 plots * 11 months = 176 sites. Since in 3 of these there were no
species, I only have 173 sites.

dataset.plot.env[1:5,]
  ID Area Treatment Block BlockID Month
1  1    1         1     1       1     1
2  2    1         1     2       2     1
3  3    1         1     3       3     1
4  4    2         1     4       4     1
5  5    2         1     5       5     1

block<-as.factor(Block)
month<-as.factor(Month)
area<-as.factor(Area)
treatment<-as.factor(Treatment)

### data is counts. x? are species.
dataset.plot.count[1:5,1:15]
  X5 X6 X7 X8 X9 X11 X12 X13 X14 X15 X16 X17 X18 X19 X20
1 11  2  1  0 58  10  28 137   0   0  87  18  68  10   0
2  6 10  2  0 36   1  26 192  65   0   6  35  94  14   0
3  2  0  0  0 27  41  33 394  16   0   3  14   4  16   0
4 22 54  7  0 26  42  10 275 137   4  22  10  30   1   0
5  1  5 10  0  0  19  45 599  60   0   6   3   0   5   0

library(vegan)
data1<-vegdist(dataset.plot.count,method="morisita")

## since I am using count data I chose morisita index.
## I read that first I needed to convert my data into a dissimilarity
## matrix. Or is this not necessary if I stipulate method in the adonis
## function?

m1<-adonis(data1~treatment,data=dataset.plot.env,permutation=200,method="mo
risita")
summary(m1)

If I do either of the above or the following, I get this result.
m1<-adonis(dataset.plot.count~treatment,data=dataset.plot.env,permutation=2
00,method="morisita")
summary(m1)

             Length Class      Mode
aov.tab        6    data.frame list
call           4    -none-     call
coefficients   0    -none-     NULL
coef.sites   519    -none-     numeric
f.perms      200    -none-     numeric
model.matrix 519    -none-     numeric
terms          3    terms      call
>

I am unsure exactly of what I am doing wrong or what I need to specify. I
would be grateful for any help and guidance.

I have read that I can use strata to specify a time series. If so would I
code it like this:
m1<-adonis(dataset.plot.count~treatment,data=dataset.plot.env,strata=datase
t.plot.env[,"Month"],permutation=200,method="morisita")
## This doesn't work either though.

I had originally planned on doing MRPP but having read that it is less
robust I opted for adonis. With MRPP, I was going to test the difference in
species composition between treatments at each month as I think I am unable
to test this for the whole study. Using adonis, do I need to do a number of
tests or can I simply run the following?

m1<-adonis(dataset.plot.count~treatment*month*block,data=dataset.plot.env,s
trata=dataset.plot.env[,"Month"],permutation=200,method="morisita")

I have had a look at Oksanen 2009, Multivariate Analysis of Ecological
Communities in R: vegan tutorial. I have not been able to find much more
information on adonis. Could anyone direct me to more literature please.

Any help would be much appreciated.

many thanks
Christine